Reflections on glass over transparent background disappear in the final render
There is nothing wrong with your image, so don't try to fix it.

The issue is that the render viewer in blender is broken: the viewer won't show the pixels that are both luminous and fully transparent (alpha zero, RGB not zero) from an image with associated alpha (like the reflection on a window that have no occlusion but are only luminous).

Read: How do I get the Glare node to output transparent instead of Black background and: Render Halo material with tranparent background

View your render As RGB (without alpha channel) and you will see that your information is there.



Or just composite an image over a background using alpha over.

If you are planing to do the final composite in an app that is not blender, make sure that you save as OpenEXR, to keep the integrity of your image.